Levy, Ronald M.- Department of Chemistry and Chemical Biology, Rutgers University

• Molecular Electrostatic Potentials and Partial Atomic Charges from Correlated Wave Functions: Applications to
• Monte Carlo Study of the Effect of Pressure on Hydrophobic Association
• proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS A large data set comparison of protein
• Cell, Vol. 108, 120, March 8, 2002, Copyright 2002 by Cell Press Structural Organization of Bacterial RNA
• J. Mol. Biol. (1986) 190, 227-254 Effect of Anisotropy and Anharmonicity on
• Trajectory Studies of in Flexible Molecules
• CABM Symposium Complete protein structure determination using backbone residual dipolar
• Impact of the Precision in NMR Relaxation Measurements on the Interpretation of
• AGBNP: An Analytic Implicit Solvent Model Suitable for Molecular Dynamics Simulations and
• Thermodynamic Decomposition of Hydration Free Energies by Computer Simulation: Application to Amines, Oxides, and Sulfides
• The SGB/NP Hydration Free Energy Model Based on the Surface Generalized Born Solvent Reaction Field and
• Eagleton Institute of Politics Rutgers, The State University of New Jersey
• Prediction of pKa Shifts without Truncation of Electrostatic Interactions: An Explicit Solvent Calculation for Succinic Acid
• 6756 J. Phys. Chem. 1991, 95, 6756-6758 npVe3. Schematicdiagramillustratingthe shift in the Fermi level (Q)
• J. Phys. Chem. 1989, 93,479-484 419 tend to increase the binding strength.
• MOLECULAR DYNAMICS OF MYOGLOBIN AT 298K Results from a 300-ps Computer Simulation
• Journal of Biomolecular NMR, 12: 471492, 1998. KLUWER/ESCOM
• COSTBI 863 16 Please cite this article in press as: Gallicchio E, Levy RM. Advances in all [57]>atom sampling methods for modeling proteinligand binding affinities, Curr Opin Struct Biol (2011), doi:10.1016/
• 994 J. Am. Chem. Soc. 1981, 103, 994-996 both by mass spectrometry and ZHNMR.z Thepro-S andpro-Rcyclohexanoneswere then convertedto labeled I-hexanols (Scheme
• Entropy-Enthalpy Compensation in Solvation and Ligand Binding Revisited
• Journal of Biomolecular NMR, 23: 263270, 2002. KLUWER/ESCOM
• ;;~,,~ints f,~om: Biological Application= of R=mllrt ~p~',rcscopy= Vol. 1--Raman Spectra and The
• FOR THE RECORD Correlation between 13
• Motions of an Molecular and
• Enthalpy-Entropy and Cavity Decomposition of Alkane Hydration Free Energies: Numerical Results and Implications for Theories of Hydrophobic Solvation
• Gaussian fluctuation formula for electrostatic free-energy changes in solution
• Reprinted from Nature, Vol. 300, No. 5888, pp. 197-198, I 1 November 1982 ~ Macmillan Journals Ltd., !982
• On the Nonpolar Hydration Free Energy of Proteins: Surface Area and Continuum Solvent Models for the Solute-Solvent
• December 2010 Prepared by
• Computer~ & Chemistry VoL 10, No. 3, pp. 16~-173, 1986 Printed in Great Britain
• Quasi-Harmonic Method For Studying Very Low Frequency Modes In Proteins
• Linear Interaction Energy (LIE) Models for Ligand Binding in Implicit Solvent: Theory and Application to
• J. Phys. Chem. 1995,99, 11575-11583 11575 Solvation Free Energies of Small Amides and Amines from Molecular Dynamicsmree
• Computer Simulation of Chemical and Biomolecular Systems Reprinted from Vol. 482
• Volume 136, number 3,4 CHEMICAL PHYSICS LETTERS 8 May 1987 A NEW RISM INTEGRAL EQUATION FOR SOLVATED POLYMERS
• 1370 Macromolecules 1984, 27, 1370-1374 Elderfield, D. J. J. Phys. A: Math. Gen. 1978. 2 1 , 2483; J .
• Protein folding pathways from replica exchange simulations and a kinetic network model
• Proc. NatI. Acad. Sci. USA Vol. 80, pp. 5569-5572, September 1983
• Temperature Weighted Histogram Analysis Method, Replica Exchange, and Transition Emilio Gallicchio, Michael Andrec, Anthony K. Felts, and Ronald M. Levy*
• Simple Continuous and Discrete Models for Simulating Replica Exchange Simulations of Protein Folding
• Protein Folding and Binding: Effective Potentials, Replica Exchange Simulations, and
• Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets
• Distinguishing among Structural Ensembles of the GB1 Peptide: REMD Simulations and NMR Experiments
• Conformational Dynamics of Substrate in the Active Site of Cytochrome P450 BM-3/NPG Complex: Insights from NMR Order Parameters
• Conformational Equilibrium of Cytochrome P450 BM-3 Complexed with N-Palmitoylglycine: A Replica Exchange
• Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications
• Long-Time Conformational Transitions of Alanine Dipeptide in Aqueous Solution: Continuous and Discrete-State Kinetic Models
• Molecular Cell, Vol. 14, 739751, June 18, 2004, Copyright 2004 by Cell Press Antibacterial Peptide Microcin J25 Inhibits
• Free Energy Surfaces of -Hairpin and -Helical Peptides Generated by Replica Exchange Molecular Dynamics with
• Biophysical Chemistry 109 (2004) 251260 0301-4622/04/$ -see front matter 2003 Elsevier B.V. All rights reserved.
• Distinguishing Native Conformations of Proteins From Decoys With an Effective Free Energy Estimator Based on
• Chloride Ion Hydration and Diffusion in Supercritical Water Using a Polarizable Water Masahito Kubo, Ronald M. Levy,*, Peter J. Rossky, Nobuyuki Matubayasi,| and
• Journal of Biomolecular NMR, 21: 335347, 2001. KLUWER/ESCOM
• New Linear Interaction Method for Binding Affinity Calculations Using a Continuum Solvent Model
• A Model for Studying Drying at Hydrophobic Interfaces: Structural and Thermodynamic Anders Wallqvist, Emilio Gallicchio, and Ronald M. Levy*
• Cluster Computing 6, 267278, 2003 2003 Kluwer Academic Publishers. Manufactured in The Netherlands.
• Protein Structural Motif Recognition via NMR Residual Dipolar Michael Andrec, Peicheng Du, and Ronald M. Levy*
• *Department of Crystallography, Birkbeck College, University of London, Malet Street, London WC1 7HX, UK;
• Solvent Models for ProteinLigand Binding: Comparison of Implicit Solvent
• A Bayesian Statistical Method for the Detection and Quantification of Rotational Diffusion Anisotropy from NMR Relaxation Data
• Estimation of Dynamic Parameters from NMR Relaxation Data using the LipariSzabo Model-Free Approach
• Journal of Biomolecular Structure & Dynamics, 1SSN 0739-1102
• On the local and nonlocal components of solvation thermodynamics and their relation to solvation shell models
• Theory and simulation Editorial overview
• Annu. Rev. Phys. Chem. 1998. 49:53167 Copyright c 1998 by Annual Reviews. All rights reserved
• On Finite-Size Corrections to the Free Energy of Ionic Hydration
• Large scale simulation of macromolecules in solution: Combining the periodic fast multipole method with multiple time step integrators
• Thermodynamics of the Hydration Shell. 2. Excess Volume and Compressibility of a Hydrophobic Solute
• 4180 J. Phys. Chem. 1994,98, 4180-4187 An Anisotropic Polarizable Water Model: Incorporation of All-Atom Polarizabilities into
• 10640 J. Phys. Chem. 1994, 98, 10640-10649 Thermodynamics of the Hydration Shell. 1. Excess Energy of a Hydrophobic Solute
• Dielectric and thermodynamic response of a generalized reaction field model for liquid state simulations
• Protein Engineering vol.6 no.6 pp.605-614. 1993 Global folding of proteins using a limited number of distance
• Simulation of photophysical processes of indoles in solution John D. Westbrook, Ronald M. Levy, and Karsten Krogh-Jespersen
• LETTERS TO THE EDITOR i7te Letfers to the Editor section is divided into four categoriesentitled Communications, Notes, Comments, and Errata.
• Biochemistry 1992,31, 10083-10093 10083 Molecular Dynamics Simulation of Solvated Protein at High Pressuret
• Volume 179, number 1,2 CHEMICAL PHYSICS LETTERS 12 Apri! 1991 Molecular dynamics simulations of water with Ewald summation
• Chemical Physics 158 ( 1991 ) 295-301 North-Holland
• J. Phys. Chem. 1990, 94, 8401-8403 8401 1 1 1 1 I I I 1 1
• Conserving Energy during Molecular Dynamics Simulations of Water, Proteins, and Proteins in Water
• J. Mol. Biol. (1990) 214, 711-736 Determining Local Conformational Variations in DNA
• Volume 166, number 4 CHEMICAL PHYSICS LETTERS 2 March 1990 MOLECULAR MECHANICS PARAMETERS FOR ELECTRONICALLY EXCITED STATES
• 6948 J. Am. Chem. SOC.1989, 111, 6948-6956 stronger interaction between the orbitals of the benzene ring and
• Volume 154, number 6 CHEMICAL PH~:SI~3 LETTERS 10 February 1989 SIMPLE MODELS FOR SOLVATION EFFECTS ON ELECTRONIC TRANSITION ENERGIES
• Viewing the Born Model for Ion Hydration through a Microscope
• DETERMINATION OF PROTEIN STRUCTURES
• Volume 144, number 3 CHEMICAL PHYSICS LETTERS 26 Februm2~ 1988 VARIABLE QUADRATIC PROPAGATOR FOR QUANTUM MONTE CARLO SIMULATIONS
• J. h'd. Riol. (1986) 190. 699-712 Temperature-dependent Molecular Dynamics and
• J. Phys. Chem. 1984,88, 4233-4238 4233 Quasi-Harmonic Method for Calculating Vibrational Spectra from Classical Simulations
• J. Am. Chem. SOC.1982, 104, 2073-2075 2073 Figure 2. Stereoscopic view of the [Cu5Ph6]-cluster as found in the [Li(PMDTA)(THF)]+ salt. This molecular plot is drawn in a different orientation
• Proc. Natt Acad. Sci. USA Vol. 79, pp. 1346-1350, February 1982
• CorreIated Helix-CoiI Transitions in Polypeptides In past discussions of the growth or decay of a polypeptide a-helix in solution; it has usually
• Molecular Simulations in Computational Biology BioMaPS 513 and Chemistry 544
• Chemistry 544 References & Reprint Folder M. P. Allen and D. J. Tildesley
• FISICA CLASSICA E QUANTISTICA Franco Battaglia
• New Computational Methods Determination in Solution
• Journal of Theoretical Biology 232 (2005) 427441 Inference of signaling and gene regulatory networks by steady-state
• Journal of Biomolecular NMR, 4 (1994) 307-324 J-Bio NMR 174
• Volume 65, number 1 CHEMICAL PHYSICS LETTERS 1 August 1979 DIFFUSIVE LANGEVIN DYNAMICS OF MODEL ALKANES *
• DIPOLAR NMR RELAXATION OF NONPROTONATED AROMATIC CARBONS IN PROTEINS
• Journal of Biomolecular NMR, 18: 83100, 2000. KLUWER/ESCOM
• Conformational Equilibria and Free Energy Profiles for the Allosteric Transition of the Ribose-binding Protein
• Helix-Coil Transitions in a Simple Polypeptide J. A. McCAMMON and S. H. NORTHRUP, Department of Chemistry,
• 4470 J . Phys. Chem. 1990, 94. 4410-4416 Molecular Dynamics Simulation of Time-Resolved Fluorescence and Nonequilibrium
• HIV-1 Reverse Transcriptase Structure with RNase H Inhibitor Dihydroxy Benzoyl Naphthyl Hydrazone
• Recent Theoretical and Computational Advances for Modeling Protein-Ligand Binding Affinities
• Simulating replica exchange simulations of protein folding with a kinetic network model
• The book is divided into sections that deal with fluvial, aeolian, and chemical sediments
• 13 December1996 Chemical PhysicsLetters263 (1996) 521-529
• 1082 J. Phys. Chem. 1991, 95, 1082-1089 albedo i s j = 12.6 X IO4 s-l, 17% (24%) lower than our value.
• Direct Determination of Kinetic Rates from Single-Molecule Photon Arrival Trajectories Using Hidden Markov Models
• Chemical Physics 171 (1993) 97-106 North-Holland
• Journal of Biomolecular NMR, 6 (1995) 221-226 J-Bio NMR 307
• Functional Group Contributions to Partial Molar Compressibilities of Alcohols in Water Daren M. Lockwood and Peter J. Rossky*
• Asynchronous Replica Exchange for Molecular Simulations EMILIO GALLICCHIO,1
• research papers Acta Cryst. (2008). D64, 383396 doi:10.1107/S090744490800070X 383
• DIFFUSIVE DYNAMICS OF ALKANE CHAINS Ronald M. Levy
• regions at the active site of enzymes with a cobalt(II1) complex, as an extension of the present study, which is also encouraged by
• Biochemistry 1989, 28, 9361-9372 9361 Solution Structures of Proteins from NMR Data and Modeling: Alternative Folds
• ELSEVIER Biophysical Chemistry 51 (1994) 235-241 Biophysical
• PROTEINS: Structure, Function, and Genetics 20:85-97 11994) Intrinsic PKaS of Ionizable Residues in Proteins: An
• Peicheng Du, Michael Andrec and Ronald M.Levy1 Department of Chemistry and Chemical Biology and BioMaPS Institute,
• JOURNAL OF MAGNETIC RESONANCE 97, 398-410 (1992) Simulating the Effect of the Two-Spin Approximation on the
• Analysis of Side-Chain Conformational Distributions in Neutrophil Peptide-5 NMR Structures
• Downloaded 22 Oct 2009 to 128.6.69.52. Redistribution subject to AIP license or copyright; see http://jcp.aip.org/jcp/copyright.jsp Downloaded 22 Oct 2009 to 128.6.69.52. Redistribution subject to AIP license or copyright; see http://jcp.aip.org/jcp/copyr
• Quantum Dynamics in Condensed Phases by Maximum Entropy Analytic Continuation of Euclidean Time
• Dobson, C. M. 1977. The structure oflysozyme in solution. In NMR in Biology. R. A. Dwek, I. D. Campbell, R. E. Richards, and R. J. P. Williams, editors. Academic Press, London. 63.
• J. Am. Chem. Sot. 1984, 106, 1923-1930 1923 Motional Averaging of Proton Nuclear Overhauser Effects
• On finite-size effects in computer simulations using the Ewald potential Francisco Figueirido, Gabriela S. Del Buono, and Ronald M. Levy
• Computer Simulations of Protein Dynamics: Theory and Experiment
• Prediction of Protein Loop Conformations Using the AGBNP Implicit Solvent Model and Torsion Angle
• Distance-Restrained Docking of Rifampicin and Rifamycin SV to RNA Polymerase Using Systematic FRET Measurements: Developing
• EvaluaLing Polarizable Potentials on Distributed Memory Parallel Computers
• Visualization of energetics and conformations from molecular
• A New One-Hour Documentary By Tami Gold THIS NEW FILM tells the story of Charlotte Bunch, from idealistic young civil rights organizer to lesbian
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• Rutgers University: Intercampus Bus Schedule Fall 2011 -Spring 2012 Semesters Sundays (Page 1/1) AS OF: 8/2011
• r XXXX American Chemical Society A dx.doi.org/10.1021/ci200194w |J. Chem. Inf. Model. XXXX, XXX, 000000 pubs.acs.org/jcim
• Provided for non-commercial research and educational use only. Not for reproduction, distribution or commercial use.
• Chichen Itza Blue (1986) by Igael Tumarkin Donated by Philip and Muriel Berman, this work
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• Reagent-Controlled Asymmetric Homologation of Boronic Esters by
• Protein hydration and unfolding --insights from experimental partial specific volumes and unfolded protein models
• 10.1021/ol103170y r 2011 American Chemical Society Published on Web 02/21/2011
• Proc. Natl Acad. Sci. USA Vol. 79, pp. 4545-4549, August 1982
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